We estimated that all upper-caste populations, except MPB from Northeast India, started to practice endogamy about 70 generations ago (Table 3). The length distributions of the AAA blocks and the ASI blocks within any one of these populations (GBR, WBR, IYR) were very similar (SI Appendix, section 5). The most parsimonious explanation of this is that the practice of gene flow between ancestries in India came to an abrupt end about 1,575 y ago (assuming 22.5 y to a generation). This time estimate belongs to the latter half of the period when the Gupta emperors ruled large tracts of India (Gupta Empire, 319–550 CE).
We have provided evidence that gene flow ended abruptly with the defining imposition of some social values and norms. The reign of the ardent Hindu Gupta rulers, known as the age of Vedic Brahminism, was marked by strictures laid down in Dharmasastra—the ancient compendium of moral laws and principles for religious duty and righteous conduct to be followed by a Hindu—and enforced through the powerful state machinery of a developing political economy (15). These strictures and enforcements resulted in a shift to endogamy. The evidence of more recent admixture among the Maratha (MRT) is in agreement with the known history of the post-Gupta Chalukya (543–753 CE) and the Rashtrakuta empires (753–982 CE) of western India, which established a clan of warriors (Kshatriyas) drawn from the local peasantry (15). In eastern and northeastern India, populations such as the West Bengal Brahmins (WBR) and the TB populations continued to admix until the emergence of the Buddhist Pala dynasty during the 8th to 12th centuries CE. The asymmetry of admixture, with ANI populations providing genomic inputs to tribal populations (AA, Dravidian tribe, and TB) but not vice versa, is consistent with elite dominance and patriarchy. Males from dominant populations, possibly upper castes, with high ANI component, mated outside of their caste, but their offspring were not allowed to be inducted into the caste. This phenomenon has been previously observed as asymmetry in homogeneity of mtDNA and heterogeneity of Y-chromosomal haplotypes in tribal populations of India (6) as well as the African Americans in United States (34).